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Update mapss logic to handle masks #137

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Update mapss logic to handle masks #137

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11 changes: 9 additions & 2 deletions dosma/scan_sequences/mri/mapss.py
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Original file line number Diff line number Diff line change
Expand Up @@ -223,13 +223,20 @@ def __fitting_helper(
ys = [vol for _, vol in echo_info]

# only calculate for focused region if a mask is available, this speeds up computation
mask = tissue.get_mask()
if mask_path is not None:
if tissue is not None:
mask = tissue.get_mask()
elif mask_path is not None:
mask = (
fio_utils.generic_load(mask_path, expected_num_volumes=1)
if isinstance(mask_path, (str, os.PathLike))
else mask_path
)
else:
mask = MedicalVolume(
volume=np.zeros_like(self.volumes[0].volume),
affine=volumes[0].affine,
headers=deepcopy(volumes[0].headers())
)

mef = MonoExponentialFit(
bounds=bounds,
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